Plots for survival models

Plots for survival models

survPlots(
  model,
  time,
  df,
  eventVar = "Event",
  timeVar = "Time",
  plotType = "ROC",
  xlim = c(0, 1),
  ylim = c(0, 1),
  colour = "black",
  harm = 0
)

Arguments

model

CoxPH model object

time

Time point to show performance at

df

Data contained in data frame

eventVar

Name of the event variable in df

timeVar

Name of the time variable in df

plotType

One of "ROC", "Calibration", or "Decision"

xlim

Limit of the x-axis for "Calibration" or "Decision"

ylim

Limit of the y-axis for "Calibration"

colour

Colour of the plot line

harm

Harm of the model for the decision curve

Value

GGPlot object

Examples

# Example using Rotterdam breast cancer data
library(survival)
mod <- coxph(Surv(rtime, recur) ~ age+meno+grade+size, data = rotterdam)
head(rotterdam)
#>      pid year age meno  size grade nodes pgr  er hormon chemo rtime recur dtime
#> 1393   1 1992  74    1  <=20     3     0  35 291      0     0  1799     0  1799
#> 1416   2 1984  79    1 20-50     3     0  36 611      0     0  2828     0  2828
#> 2962   3 1983  44    0  <=20     2     0 138   0      0     0  6012     0  6012
#> 1455   4 1985  70    1 20-50     3     0   0  12      0     0  2624     0  2624
#> 977    5 1983  75    1  <=20     3     0 260 409      0     0  4915     0  4915
#> 617    6 1983  52    0  <=20     3     0 139 303      0     0  5888     0  5888
#>      death
#> 1393     0
#> 1416     0
#> 2962     0
#> 1455     0
#> 977      0
#> 617      0
survPlots(
  model = mod,
  time = 2000,
  df = rotterdam,
  eventVar = "recur",
  timeVar = "rtime",
  plotType="ROC")
#> Setting levels: control = 0, case = 1
#> Setting direction: controls < cases
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.


survPlots(
  model = mod,
  time = 2000,
  df = rotterdam,
  eventVar = "recur",
  timeVar = "rtime",
  plotType="Calibration")
#> `geom_smooth()` using formula = 'y ~ x'


survPlots(
  model = mod,
  time = 2000,
  df = rotterdam,
  eventVar = "recur",
  timeVar = "rtime",
  plotType="Decision")
#> Warning: Removed 1 row containing missing values (`geom_line()`).
#> Warning: Removed 1 row containing missing values (`geom_line()`).


survPlots(
  model = mod,
  time = 2000,
  df = rotterdam,
  eventVar = "recur",
  timeVar = "rtime",
  plotType="All")
#> Setting levels: control = 0, case = 1
#> Setting direction: controls < cases
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> `geom_smooth()` using formula = 'y ~ x'
#> Warning: Removed 1 row containing missing values (`geom_line()`).
#> Warning: Removed 1 row containing missing values (`geom_line()`).